A chromosome-level genome assembly of an elite indica breeding line resolves the genomic architecture of drought-yield QTLs qDTY2.2 and qDTY4.1 in rice.
7 affiliations
- 1Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea.
- 2IRRI-Korea Office, International Rice Research Institute, Wanju, Republic of Korea.
- 3Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea.
- 4Supercomputing Center, Agricultural Biotechnology Department, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea.
- 5Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
- 6Department of Research and Development, DNACARE Co. Ltd., Seoul, Republic of Korea.
- 7Institute for Advanced Plant Breeding and Phytochemicals (IAPBP), Sejong University, Seoul, Republic of Korea.
Abstract
Drought-yield quantitative trait loci (QTLs) qDTY2.2 and qDTY4.1 improve grain yield under reproductive-stage drought in rice (Oryza sativa L.), yet their genomic architecture remains poorly resolved in elite indica breeding backgrounds. We generated a chromosome-level assembly of IR87707-446-B-B-B (IR64-qDTY2.2 + qDTY4.1), which carries both QTLs in the IR64 background, and delineated donor-derived introgressions using informative parental single-nucleotide polymorphisms (SNPs). The 395.5-Mb assembly comprised 12 chromosomes, showed 99.2% BUSCO completeness, and contained 40,189 predicted protein-coding genes. Informative-SNP analysis, supported by read-depth assessment of low-information regions, resolved qDTY2.2 and qDTY4.1 as continuous donor-derived introgressions containing 194 and 97 genes, respectively. Comparative genome analysis showed that qDTY2.2 was largely macrostructurally collinear with IRGSP-1.0, whereas qDTY4.1 showed pronounced structural divergence and contained a 15.6-kb inversion relative to IR64sj. Comparative gene-content analysis further showed that 37.1% and 55.7% of genes in qDTY2.2 and qDTY4.1, respectively, lacked collinear orthologs in IRGSP-1.0. Multi-accession allele analysis revealed contrasting candidate-gene profiles between the two loci. Six of eight qDTY2.2 candidates had coding sequences identical to IR64sj, whereas all four qDTY4.1 candidates showed coding differences from IR64sj. Coordinate-based SNP markers were also developed for donor-haplotype tracking across both QTL intervals. These results provide a genome-resolved framework for characterizing drought-yield QTLs and developing breeding-background-specific markers for recombination-aware rice breeding.
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BibTeX
@article{han2026chromosomelevel,
title = {{A chromosome-level genome assembly of an elite indica breeding line resolves the genomic architecture of drought-yield QTLs qDTY2.2 and qDTY4.1 in rice.}},
author = {Jae-Hyuk Han and Na-Hyun Shin and Keunpyo Lee and Yohei Koide and Yeisoo Yu and Il-Ryong Choi and Joong Hyoun Chin},
journal = {The plant genome},
year = {2026},
month = oct,
doi = {10.1002/tpg2.70330},
url = {https://europepmc.org/article/MED/42920244},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - A chromosome-level genome assembly of an elite indica breeding line resolves the genomic architecture of drought-yield QTLs qDTY2.2 and qDTY4.1 in rice.
AU - Jae-Hyuk Han
AU - Na-Hyun Shin
AU - Keunpyo Lee
AU - Yohei Koide
AU - Yeisoo Yu
AU - Il-Ryong Choi
AU - Joong Hyoun Chin
PY - 2026
DA - 2026/10/30
JO - The plant genome
DO - 10.1002/tpg2.70330
UR - https://europepmc.org/article/MED/42920244
AB - Drought-yield quantitative trait loci (QTLs) qDTY2.2 and qDTY4.1 improve grain yield under reproductive-stage drought in rice (Oryza sativa L.), yet their genomic architecture remains poorly resolved in elite indica breeding backgrounds. We generated a chromosome-level assembly of IR87707-446-B-B-B (IR64-qDTY2.2 + qDTY4.1), which carries both QTLs in the IR64 background, and delineated donor-derived introgressions using informative parental single-nucleotide polymorphisms (SNPs). The 395.5-Mb assembly comprised 12 chromosomes, showed 99.2% BUSCO completeness, and contained 40,189 predicted protein-coding genes. Informative-SNP analysis, supported by read-depth assessment of low-information regions, resolved qDTY2.2 and qDTY4.1 as continuous donor-derived introgressions containing 194 and 97 genes, respectively. Comparative genome analysis showed that qDTY2.2 was largely macrostructurally collinear with IRGSP-1.0, whereas qDTY4.1 showed pronounced structural divergence and contained a 15.6-kb inversion relative to IR64sj. Comparative gene-content analysis further showed that 37.1% and 55.7% of genes in qDTY2.2 and qDTY4.1, respectively, lacked collinear orthologs in IRGSP-1.0. Multi-accession allele analysis revealed contrasting candidate-gene profiles between the two loci. Six of eight qDTY2.2 candidates had coding sequences identical to IR64sj, whereas all four qDTY4.1 candidates showed coding differences from IR64sj. Coordinate-based SNP markers were also developed for donor-haplotype tracking across both QTL intervals. These results provide a genome-resolved framework for characterizing drought-yield QTLs and developing breeding-background-specific markers for recombination-aware rice breeding.
SN - 1940-3372
ER -